Chuck vs The Secret
by YellowShadess
Summary: Besides the fact that Mary Bartowski was a spy, she kept an even bigger secret from her children. What will Chuck do when he finds out a secret that his mother has been keeping from him and Ellie for 20 years? Set in Season 4 between the engagement and the wedding.
1. Chapter 1

**Hey guys! YellowShadess here with a new story! I just finished watching Chuck and I am completely obsessed with this show. Zachary Levi's face is pure perfection and the story is amazing! I was hooked on the first episode and I cried my eyes out on the last. i thought this story up when I was in the middle of the show and I want to write it out before I lose it! Besides the fact that Mary Bartowski was a spy she kept an even bigger secret from her children. What will Chuck do when he finds out a secret that his mother has been keeping from him and Ellie for 20 years? Set in Season 4 between the engagement and the wedding. Here we go!**

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Chuck woke up to find the bed empty. He sat up and smelled something cooking. He got up and walked down the hall to the kitchen where he found Sarah making breakfast. She was wearing a baggy t-shirt and slippers. He moved behind her and hugged her from behind. She turned around and kissed him softly. They broke from the kiss and Sarah continued cooking. Chuck leaned against the counter and watched her. His like was going surprisingly well; he was engaged to the most amazing and the most badass woman in the world, he had a brand new niece, the intersect was working perfectly in his mind. Everything was perfect for the first time in 4 years. As he made coffee he spoke,

"So, wanted to play Martha Stewart again?" He said laughing softly. He felt a playful slap on the arm from Sarah.

"Shut up. I thought it would be nice to have a real breakfast and to relax in bed all day because today is our day off in a long time." She said as she finished flipping pancakes and cooking bacon. Chuck placed a cup of coffee next to her and kissed her cheek. She smiled up at him and took all the food to the table. As they were sitting down they heard a knock at the door. Chuck went to open the door and saw Ellie standing in the door way holding baby Clara.

"Why hello sister! What brings you here?" He asked. Ellie smiled softly and spoke,

"Chuck, we need to talk." She said. Chuck's smile faded quickly and he nodded. Sarah sensed that something was wrong and stood up.

"I can watch Clara as you two speak." She said. Ellie smiled and handed the infant to her future sister in law and guided Chuck outside. They sat down on the fountain and Ellie sighed,

"Elle, whats going on? You're scaring me." Chuck said nervously. Ellie looked up at him and spoke,

"Chuck, you know how dad left me his car right?" he nodded, "Well, I found a computer under the driver seat." Chucks eyes widened

"The Orion computer." He said. Ellie looked puzzled,

"Yes, how did you kno-" she looked up at him, "You knew I had the computer." She said. Chuck nodded in defeat,

"Yes I knew, Awesome told me about it. Why didn't you tell me?" He asked. She broke eye contact.

"I didn't want you to get involved in the spy life again." She said. She looked up and saw that his eyes were widen like he was hiding something.

"Chuck, why are you hiding?" She said.

"Well..." She broke him off,

"You're still a spy aren't you?" She asked angrily. He nodded. She sighed

"Why didn't you tell me that you were still a spy!? Do you know how dangerous that is!" She said angrily. He looked up at her and spoke with the same angry tone,

"Why didn't you tell me you had one of dads computers?! You have no idea how dangerous that computer is!" He said. She sighed

"You're right." They both calmed down and Chuck spoke,

"Did you find anything?" He asked. She nodded

"Yes, that is what I came to talk to you about. In the computer there were files hidden. I've cracked the code and gained access to the files. Chuck, they were files on us. You, me and mom." She said. Chuck looked puzzled,

"Why would files about us be on the orion computer?" She shrugged her shoulders,

"I have no clue but I read them and they contained everything about our lives; our birth certificates, school records, medical records, school photos and so much more were on there. He kept records of us before and after he left. Mom too, everything that had to do with her was in the file." She said. Chuck nodded,

"No offense sis but what is the big deal? He probably wanted to keep tabs on us after he left." He said. Ellie shook her head.

"I got why our files were on the computer but I came across another file names 'Louise'. I opened it and saw two items, one was a picture of a baby and the other was a birth certificate; everything was blacked out except for a first name, date of birth and mothers first initial; Louise, born March 24th 1992, Mother's initial M." Chuck looked at his sister with confusion.

"Ellie, what does that mean?" He asked. She made eye contact with his and spoke,

"Chuck, why would dad have a file on an unknown woman with his personal files? Why would he have a birth certificate of a woman born almost 10 months after mom left with no last name and her mother's initial of 'M'?" She said. Chuck, in realization looked up at his sister,

"Ellie... what are you trying to say?" He asked. She sighed and spoke,

"Chuck, I think we have a sister."

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 **I hope you enjoyed this chapter! I will write more soon but with the end of the semester only 10 days away I might push off writing until after finals! I'll hopefully post more ASAP! -J.A.**


	2. Chapter 2

**Hey guys! I'm glad you guys like the story! I'm sorry I haven't updated in a while but I am back with more! Here is Chapter 2!**

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Chuck stared at his sister in complete shock. Another sister? One that was 20 years old; already an adult. He was mind blown.

"Chuck?" Ellie said. Chuck was pulled out from his daze. He looked up at his sister in shock,

"What do we do?" He was truly confused,

"Well, we have to figure this out. We have to find her." She said. Chuck nodded,

"But how? There is no information about her in this file and I highly doubt that she has the same last name as us." He said somewhat frantic. Ellie nodded in agreement. She sighed and spoke

"Well, I can keep digging through the computer to see if anything else pops up about her," Chuck spoke

"What if we can't find anything?" He asked doubtful. Ellie looked at her brother with determination in her eyes and spoke,

"We are going to have to go to the source then." She said. Chuck's eyes widened.

"You want to ask mom about the baby she gave up 20 years ago and didn't tell us about? Oh yeah thats going to go over smoothly." He said sarcastically, she slapped his arm slightly

"I'm serious Chuck. If we are going to find this girl then we have to use all of our resources. For now lets use what we have; the computer and your spy resources. We can use them to figure out who this 'Louise' is and finally meet her and if all else fails we will ask mom." Chuck nodded as they made their plan to find their long lost sister. They got up and went into Chuck's apartment to enlist the help of Sarah and the CIA. They walked inside and saw Sarah rocking baby Clara and whispering to her softly. Chuck's heart fluttered, Sarah is going to make a great mother to their children someday. He made his presence known. She looked up and smiled at the siblings. Chuck smiled back at her and spoke

"Sarah we need help." He said. Her smiled disappeared slightly

"Is everything okay?" She asked. Chuck nodded and proceeded to tell her about their possible long lost sister and that they need to find her. Sarah was shocked. She couldn't believe that she could have another sister in law. With determination in her eyes she grabbed her laptop and went to work taking every bit of information and plugging it into the CIA database. Her fingers flew across the keyboard as Ellie worked on the Orion computer trying to find more information on the woman. They worked for hours; only stopping for bathroom and food breaks. As dusk came around and no such luck the group decided to call it a day and work on it more tomorrow. They were going to need a lot more help if they were going to find more information on the mysterious girl. They would enlist the help of Casey and use the NSA database to find some information and Ellie was going to go through the hospital database to find a birth certificate or something that would lead them to her. Ellie went home and Chuck and Sarah went to bed. Sarah fell asleep but Chuck wasn't able to find rest. He couldn't get his possible long lost sister off of his mind. Why did his mother give her up for adoption? What if they find her and she doesn't want to be apart of the family? So many questions flew through his mind. Just as 3 am rolled around and Chuck was still awake he heard a noise. He woke Sarah up and they sprang into action. They quietly creeped around the house in an effort to see who had broken in. Chuck checked the back of the house and Sarah checked the front. Chuck was checking the back room when Sarah called him to the front. He went and saw his fiancé standing with his mother.

"Mom. What are you doing here?" He asked. She looked mad

"Chuck why are you looking for Lousie?" She asked sternly. They both looked at her confused

"How do you know that we are looking for her?" He asked

"I have my sources." She said putting her hands on her hips. Chuck groaned and spoke

"Ellie called you and asked about her didn't she?" He asked annoyed. She nodded softly. Chuck sighed in frustration and sat on the couch.

"Mom, why are you here?" He asked.

"Chuck, you have to stop looking for Louise. Finding her can put you guys in a lot of danger." She said. He looked at her puzzled,

"Why? What's so dangerous about finding a 20 year old girl?" He asked. Mary shook her head in response.

"Chuck. You don't understand. She was put up for adoption for a reason. If you keep digging you will find things that are too dangerous to know. Please stop looking." She said. She got up, hugged her son and left the couple confused. Chuck sat down on the couch defeated. Sarah sat next to him and rubbed his shoulder. She hugged him and spoke "What do you want to do Chuck? Let it go or keep looking?" She asked. He looked at her and spoke

"We keep looking. When has the threat of danger ever stop us?" He said. She smiled at his enthusiasm. She kissed his forehead and got up.

"Okay, we will continue tomorrow. Let's go get so,e rest. We have a lot of work tomorrow. " she stuck out her hand and he grabbed it. The journeyed hand in hand to the bedroom for some rest.

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 **I hope you enjoyed this chapter! I will try to update more frequently from now on! See ya** **on the flipside! -J.A.**


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